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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D. C. 20549

FORM 10-Q/A

(Amendment No. 1)

For the quarterly period ended June 30, 2013

or

For the transition period from                      to                     

Commission File Number 000-51820

ALEXZA PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

(Registrant’s telephone number, including area code): (650) 944-7000

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ¨    No  x

Total number of shares of common stock outstanding as of August 1, 2013: 17,235,086.

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Explanatory Note

This Amendment No. 1 to the quarterly report of Alexza Pharmaceuticals, Inc. on Form 10-Q/A (this “Form 10-Q/A”) amends our quarterly report on Form 10-Q for the period ended June 30, 2013, which was originally filed with the Securities and Exchange Commission (“SEC”) on August 14, 2013 (the “Original Form 10-Q”). This Form 10-Q/A is being filed (a) in response to a comment letter we received from the SEC in connection with its review of Exhibit 10.4 to the Original Form 10-Q and (b) solely for the purpose of amending Item 6 of Part II of the Original Form 10-Q and the Exhibit Index to the Original Form 10-Q to reflect the filing of a revised version of Exhibit 10.4 herewith. As indicated herein, confidential treatment has been requested from the SEC with respect to specific portions of such exhibit. The certifications of our principal executive officer and principal financial and accounting officer are attached to this Form 10-Q/A as Exhibits 31.3, 31.4 and 32.2. Unless the context requires otherwise, references in this Form 10-Q/A to “Alexza,” “we” and “our” refer to Alexza Pharmaceuticals, Inc.

Except as described above, no other changes have been made to the Original Form 10-Q, and this Form 10-Q/A does not amend, update or change the financial statements or disclosures in the Original Form 10-Q. This Form 10-Q/A does not reflect events occurring after the filing of the Original Form 10-Q or modify or update those disclosures. Accordingly, this Form 10-Q/A should be read in conjunction with our filings made with the SEC subsequent to the filing of the Original Form 10-Q, including any amendments to those filings.

ALEXZA PHARMACEUTICALS, INC.

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PART II. OTHER INFORMATION

Item 6. Exhibits

See the Exhibit Index following the signature page to this Form 10-Q/A for a list of exhibits filed or furnished with this report, which Exhibit Index is incorporated herein by reference.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

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EXHIBIT INDEX

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